Beta diversity

Between-sample variability from 16S rRna-gene sequencing data.

Clustering

PCA

Clustering by timepoint (PCA):

Clustering by treatment (PCA): by timepoints

Before_oil 

## Saving 7 x 5 in image

After_oil 

## Saving 7 x 5 in image

MDS

Clustering by treatment (MDS): NMDS1 vs NMDS2

## Warning in metaMDS(matxTP, k = 3): stress is (nearly) zero: you may have
## insufficient data

Clustering by timepoint (MDS):

NMDS1 vs NMDS2

## Warning in metaMDS(matx, k = 3): stress is (nearly) zero: you may have
## insufficient data

Clustering by type (MDS): NMDS1 vs NMDS3

Clustering by type (MDS): NMDS2 vs NMDS3

Clustering by treatment by timepoint (MDS):

## Warning in metaMDS(matx): stress is (nearly) zero: you may have insufficient
## data

Significance of between-group distances

Significance values based on permuted analysis of variance (999 permutations), repeated 100 times.

Below the ANOVA table from the model:

\[ X = \mu + treatment + timepoint + treatment*type + e \]

Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
treatment 1 0.1439951 0.1439951 1.313483 0.0417820 0.128
timepoint 1 0.1231220 0.1231220 1.123084 0.0357254 0.254
treatment_by_timepoint 29 3.1792253 0.1096285 NA 0.9224926 NA
residuals 31 3.4463424 NA NA 1.0000000 NA

going 3D

## Run 0 stress 0.0001263224 
## Run 1 stress 9.891639e-05 
## ... New best solution
## ... Procrustes: rmse 0.00018548  max resid 0.0006609065 
## ... Similar to previous best
## Run 2 stress 9.998749e-05 
## ... Procrustes: rmse 9.377306e-05  max resid 0.0002382569 
## ... Similar to previous best
## Run 3 stress 9.846708e-05 
## ... New best solution
## ... Procrustes: rmse 0.0001415423  max resid 0.000499575 
## ... Similar to previous best
## Run 4 stress 9.953504e-05 
## ... Procrustes: rmse 0.0001596566  max resid 0.0005405929 
## ... Similar to previous best
## Run 5 stress 9.852399e-05 
## ... Procrustes: rmse 3.578719e-05  max resid 0.0001329834 
## ... Similar to previous best
## Run 6 stress 9.996312e-05 
## ... Procrustes: rmse 1.900173e-05  max resid 7.960467e-05 
## ... Similar to previous best
## Run 7 stress 9.904341e-05 
## ... Procrustes: rmse 1.954365e-05  max resid 9.126139e-05 
## ... Similar to previous best
## Run 8 stress 9.794829e-05 
## ... New best solution
## ... Procrustes: rmse 0.0001054845  max resid 0.0002977778 
## ... Similar to previous best
## Run 9 stress 9.944269e-05 
## ... Procrustes: rmse 0.0001083153  max resid 0.0003207916 
## ... Similar to previous best
## Run 10 stress 9.844764e-05 
## ... Procrustes: rmse 0.0001197334  max resid 0.0004473062 
## ... Similar to previous best
## Run 11 stress 9.744944e-05 
## ... New best solution
## ... Procrustes: rmse 7.03499e-05  max resid 0.0003191853 
## ... Similar to previous best
## Run 12 stress 9.496812e-05 
## ... New best solution
## ... Procrustes: rmse 0.0001236837  max resid 0.0005617767 
## ... Similar to previous best
## Run 13 stress 9.841598e-05 
## ... Procrustes: rmse 0.0001488383  max resid 0.000560692 
## ... Similar to previous best
## Run 14 stress 9.785192e-05 
## ... Procrustes: rmse 0.0001435198  max resid 0.000556119 
## ... Similar to previous best
## Run 15 stress 9.809965e-05 
## ... Procrustes: rmse 0.0001370057  max resid 0.0004814745 
## ... Similar to previous best
## Run 16 stress 0.0001599563 
## ... Procrustes: rmse 0.0002432481  max resid 0.0008920106 
## ... Similar to previous best
## Run 17 stress 9.675082e-05 
## ... Procrustes: rmse 0.0001120027  max resid 0.0003662987 
## ... Similar to previous best
## Run 18 stress 9.677233e-05 
## ... Procrustes: rmse 0.0001646299  max resid 0.0006686248 
## ... Similar to previous best
## Run 19 stress 9.428191e-05 
## ... New best solution
## ... Procrustes: rmse 0.0001440906  max resid 0.0004131426 
## ... Similar to previous best
## Run 20 stress 9.992988e-05 
## ... Procrustes: rmse 7.914129e-05  max resid 0.0002852179 
## ... Similar to previous best
## *** Solution reached

before_oil

after_oil